Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012359.1 Corchorus olitorius cultivar O-4 contig12392, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 957
Length: 1595
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Found at i:860 original size:333 final size:332
Alignment explanation
Indices: 1--1595 Score: 2434
Period size: 333 Copynumber: 4.8 Consensus size: 332
* *
1 GTCG-AAAAAATTGGGGAAAAACTTTTCGGGTTAG-TTTTTCCAAATTTTAGCCCAAATCGTGTA
1 GTCGCAAAAAATTGGGGAAAAACTTTTCGGGTCAGTTTTTTCCAAATTTTAGCCGAAATCGTGTA
* *
64 CTAACCATCACGATTTTTGGCTAAAAATGCGTTTCGGGGACCTGACTCAGTTTTGCATGATTTTT
66 CTAACCATCACGGTTTTTGGCTAAAAATGCGTTTC-GGGCCCTGACTCAGTTTTGCATGATTTTT
* *
129 GGCAGTAAGACTTCTCGAAATATCTATATAT-ATCTAATCAAATCTCTAAGCCACAATGGATTTA
130 GGCAGAAAGACTTCTCGAAATATCTATAT-TCATCTAATCAAATCTCTCAGCCACAATGGATTTA
*
193 CGGATTTATTTTTACGAGTATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCAGAAGAAAA
194 CGGATTTATTTTTACGAGTATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCAGAAAAAAA
*
258 TGGAAAAACGATATTAGAAGCGTGAAACACCCTAAAATATTTTTGGCGTTGAATTATATGATTTT
259 TGGAAAAACGAAATTAGAAGCGTGAAA-ACCCTAAAATATTTTTGGCGTTGAATTATATGATTTT
323 TCTGAGTATT
323 TCTGAGTATT
* * * ** * * * *
333 GTGGCCAAATAATTGTGGAAAAACTTTTCGCATCAGGATTTTGCAAAATTTTAGCCGAAATAGTG
1 GTCG-CAAAAAATTGGGGAAAAACTTTTCGGGTCA-GTTTTTTCCAAATTTTAGCCGAAATCGTG
* * *
398 TACTAACCATCACGGTTTTTGGCTAAAAATACGTTTCGGGTCCTTGACTCTGTTTTGCAAT-ATT
64 TACTAACCATCACGGTTTTTGGCTAAAAATGCGTTTCGGG-CCCTGACTCAGTTTTGC-ATGATT
*
462 TTTGGCAGAAAGACTTCTCGAAATATCTATATTCATCTAATCAAATCTCTCAGCCTCAATGGATT
127 TTTGGCAGAAAGACTTCTCGAAATATCTATATTCATCTAATCAAATCTCTCAGCCACAATGGATT
527 TACGGATTTATTTTTACGAGTATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCAGAAAAA
192 TACGGATTTATTTTTACGAGTATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCAGAAAAA
* * *
592 AATGGAAAAACTATATTAGAAGCGTGAAAACCCTAAAATATTTTTGGTGTTGAATTATATGATTT
257 AATGGAAAAACGAAATTAGAAGCGTGAAAACCCTAAAATATTTTTGGCGTTGAATTATATGATTT
*
657 ATCTGAGTATT
322 TTCTGAGTATT
* * *
668 GTCGCAAAATATTGTGGAAAAACTTTTCGGGTCAGTTTTTTCCAAATTTTAGCTGAAATCGTGTA
1 GTCGCAAAAAATTGGGGAAAAACTTTTCGGGTCAGTTTTTTCCAAATTTTAGCCGAAATCGTGTA
* * * * *
733 CTAACCGTCACGGTTTTTAGCTAAAAATGCATTTCGGTGCCCTGACTAAGTTTTACATGATTTTT
66 CTAACCATCACGGTTTTTGGCTAAAAATGCGTTTCGG-GCCCTGACTCAGTTTTGCATGATTTTT
* *
798 GGCAGTAAGACTTCTCGAAATATCTATATTCATCTAATCAAATCTTTCAGCCACAATGGATTTAC
130 GGCAGAAAGACTTCTCGAAATATCTATATTCATCTAATCAAATCTCTCAGCCACAATGGATTTAC
*
863 GGATTTATTTTTACGAGTATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTTCTGAAAAAAA
195 GGATTTATTTTTACGAGTATCTGAATCTTGTTTCGATTTAATTAGAAATAAA-TTCAGAAAAAAA
* *
928 AGGGAAAACGAAATTAGAAGCGTGAAAAACCCTAAAATATTTTTGGCGTTGAATTATATGATTTT
259 TGGAAAAACGAAATTAGAAGCGTG-AAAACCCTAAAATATTTTTGGCGTTGAATTATATGATTTT
* *
993 TTTAAGTATT
323 TCTGAGTATT
* * * * * *
1003 GTGGCAAAAAATT-GAGAAAAACTTTTCGGATCAATTTTTTCCAAAATTTTAACTGAAATCGTGT
1 GTCGCAAAAAATTGGGGAAAAACTTTTCGGGTCAGTTTTTTCC-AAATTTTAGCCGAAATCGTGT
* * *
1067 ATTAA-CATCACGGTTTTTGGCTAAAAATGCCTTTCGGGGCCCTGACTCAGTTTTGCA-AATTTT
65 ACTAACCATCACGGTTTTTGGCTAAAAATGCGTTTC-GGGCCCTGACTCAGTTTTGCATGATTTT
* *
1130 TGGCAGAAATACTTCTCGAAATATCTATATTCATCTAATCAAATCTCTCATCCACAATGGATTTA
129 TGGCAGAAAGACTTCTCGAAATATCTATATTCATCTAATCAAATCTCTCAGCCACAATGGATTTA
* *
1195 -GAGATTTATTTTTACTAGTATCTGAATCTTGTTTCAATTTAATTAGAAATAAATTCAGAAAAAA
194 CG-GATTTATTTTTACGAGTATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCAG-AAAAA
1259 AATGGAAAAACGAAATTAGAAGCGTGAAAATCCCTAAAATATTTTTGGCGTTGAATTATATGATT
257 AATGGAAAAACGAAATTAGAAGCGTGAAAA-CCCTAAAATATTTTTGGCGTTGAATTATATGATT
1324 TTTCTGAGTATT
321 TTTCTGAGTATT
* * *
1336 GTCGCAAAAAATTGGGGAAAAAATTTTCGGGTAAGTTTTTTTCCAAATTTTAGCCGAAATCGTGC
1 GTCGCAAAAAATTGGGGAAAAACTTTTCGGGTCAG-TTTTTTCCAAATTTTAGCCGAAATCGTGT
*
1401 ACTAACCATCACGGTTTTTGGCTAAAAAT-CGTTTCGGGCCCTGACTCACTTTTGCATGATTTTT
65 ACTAACCATCACGGTTTTTGGCTAAAAATGCGTTTCGGGCCCTGACTCAGTTTTGCATGATTTTT
1465 GGCAGAAAGACTTCTCGAAATATCTATATTCATCTAATCAAATCTCTCAGCCACAATGGATTTAC
130 GGCAGAAAGACTTCTCGAAATATCTATATTCATCTAATCAAATCTCTCAGCCACAATGGATTTAC
* *
1530 GGATTTATTTTTACGAGTATCTTAATCTTATTTCGATTTAATTAGAAATAAATTACAAGAAAAAA
195 GGATTTATTTTTACGAGTATCTGAATCTTGTTTCGATTTAATTAGAAATAAATT-C-AGAAAAAA
1595 A
258 A
Statistics
Matches: 1144, Mismatches: 96, Indels: 43
0.89 0.07 0.03
Matches are distributed among these distances:
332 14 0.01
333 412 0.36
334 311 0.27
335 176 0.15
336 229 0.20
337 2 0.00
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (332 bp):
GTCGCAAAAAATTGGGGAAAAACTTTTCGGGTCAGTTTTTTCCAAATTTTAGCCGAAATCGTGTA
CTAACCATCACGGTTTTTGGCTAAAAATGCGTTTCGGGCCCTGACTCAGTTTTGCATGATTTTTG
GCAGAAAGACTTCTCGAAATATCTATATTCATCTAATCAAATCTCTCAGCCACAATGGATTTACG
GATTTATTTTTACGAGTATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCAGAAAAAAATG
GAAAAACGAAATTAGAAGCGTGAAAACCCTAAAATATTTTTGGCGTTGAATTATATGATTTTTCT
GAGTATT
Found at i:1378 original size:669 final size:669
Alignment explanation
Indices: 1--1595 Score: 2553
Period size: 669 Copynumber: 2.4 Consensus size: 669
* *
1 GTCG-AAAAAATTGGGGAAAAACTTTTCGGGTTAG-TTTTTCCAAATTTTAGCCCAAATCGTGTA
1 GTCGCAAAAAATTGGGGAAAAACTTTTCGGGTAAGTTTTTTCCAAATTTTAGCCGAAATCGTGTA
* *
64 CTAACCATCACGATTTTTGGCTAAAAATGCGTTTCGGGGACCTGACTCAGTTTTGCATGATTTTT
66 CTAACCATCACGGTTTTTGGCTAAAAATGCGTTTC-GGGCCCTGACTCAGTTTTGCATGATTTTT
*
129 GGCAGTAAGACTTCTCGAAATATCTATATAT-ATCTAATCAAATCTCTAAGCCACAATGGATTTA
130 GGCAGTAAGACTTCTCGAAATATCTATAT-TCATCTAATCAAATCTCTCAGCCACAATGGATTTA
*
193 CGGATTTATTTTTACGAGTATCTGAATCTTGTTTCGATTTAATTAGAAATAAA-TTCAGAAGAAA
194 CGGATTTATTTTTACGAGTATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTTCAGAAAAAA
* * *
257 ATGGAAAAACGATATTAGAAGCGTGAAACACCCTAAAATATTTTTGGCGTTGAATTATATGATTT
259 AAGGAAAAACGAAATTAGAAGCGTGAAAAACCCTAAAATATTTTTGGCGTTGAATTATATGATTT
* * * * * *
322 TTCTGAGTATTGTGGCCAAATAATTGTGGAAAAACTTTTCGCATCAGGATTTTGCAAAATTTTAG
324 TTCTAAGTATTGTGGCCAAAAAATTGTAGAAAAACTTTTCGCATCAAGATTTTCCAAAATTTTAA
* * * *
387 CCGAAATAGTGTACTAACCATCACGGTTTTTGGCTAAAAATACGTTTCGGGTCCTTGACTCTGTT
389 CCGAAATAGTGTACTAACCATCACGGTTTTTGGCTAAAAATACCTTTCGGGGCCCTGACTCAGTT
452 TTGCAATATTTTTGGCAGAAAGACTTCTCGAAATATCTATATTCATCTAATCAAATCTCTCAGCC
454 TTGCAATATTTTTGGCAGAAAGACTTCTCGAAATATCTATATTCATCTAATCAAATCTCTCAGCC
* *
517 TCAATGGATTTACGGATTTATTTTTACGAGTATCTGAATCTTGTTTCGATTTAATTAGAAATAAA
519 ACAATGGATTTACGGATTTATTTTTACGAGTATCTGAATCTTGTTTCAATTTAATTAGAAATAAA
* * *
582 TTCAGAAAAAAATGGAAAAACTATATTAGAAGCGTGAAAACCCTAAAATATTTTTGGTGTTGAAT
584 TTCAGAAAAAAATGGAAAAACGAAATTAGAAGCGTGAAAACCCTAAAATATTTTTGGCGTTGAAT
647 TATATGATTTATCTGAGTATT
649 TATATGATTTATCTGAGTATT
* * * *
668 GTCGCAAAATATTGTGGAAAAACTTTTCGGGTCAGTTTTTTCCAAATTTTAGCTGAAATCGTGTA
1 GTCGCAAAAAATTGGGGAAAAACTTTTCGGGTAAGTTTTTTCCAAATTTTAGCCGAAATCGTGTA
* * * * *
733 CTAACCGTCACGGTTTTTAGCTAAAAATGCATTTCGGTGCCCTGACTAAGTTTTACATGATTTTT
66 CTAACCATCACGGTTTTTGGCTAAAAATGCGTTTCGG-GCCCTGACTCAGTTTTGCATGATTTTT
*
798 GGCAGTAAGACTTCTCGAAATATCTATATTCATCTAATCAAATCTTTCAGCCACAATGGATTTAC
130 GGCAGTAAGACTTCTCGAAATATCTATATTCATCTAATCAAATCTCTCAGCCACAATGGATTTAC
*
863 GGATTTATTTTTACGAGTATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTTCTGAAAAAAA
195 GGATTTATTTTTACGAGTATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTTCAGAAAAAAA
*
928 AGGGAAAACGAAATTAGAAGCGTGAAAAACCCTAAAATATTTTTGGCGTTGAATTATATGATTTT
260 AGGAAAAACGAAATTAGAAGCGTGAAAAACCCTAAAATATTTTTGGCGTTGAATTATATGATTTT
* * **
993 TTTAAGTATTGTGG-CAAAAAATTG-AGAAAAACTTTTCGGATCAATTTTTTCCAAAATTTTAAC
325 TCTAAGTATTGTGGCCAAAAAATTGTAGAAAAACTTTTCGCATCAAGATTTTCCAAAATTTTAAC
* * * *
1056 TGAAATCGTGTATTAA-CATCACGGTTTTTGGCTAAAAATGCCTTTCGGGGCCCTGACTCAGTTT
390 CGAAATAGTGTACTAACCATCACGGTTTTTGGCTAAAAATACCTTTCGGGGCCCTGACTCAGTTT
* *
1120 TGCAA-ATTTTTGGCAGAAATACTTCTCGAAATATCTATATTCATCTAATCAAATCTCTCATCCA
455 TGCAATATTTTTGGCAGAAAGACTTCTCGAAATATCTATATTCATCTAATCAAATCTCTCAGCCA
*
1184 CAATGGATTTA-GAGATTTATTTTTACTAGTATCTGAATCTTGTTTCAATTTAATTAGAAATAAA
520 CAATGGATTTACG-GATTTATTTTTACGAGTATCTGAATCTTGTTTCAATTTAATTAGAAATAAA
1248 TTCAGAAAAAAAATGGAAAAACGAAATTAGAAGCGTGAAAATCCCTAAAATATTTTTGGCGTTGA
584 TTCAG-AAAAAAATGGAAAAACGAAATTAGAAGCGTGAAAA-CCCTAAAATATTTTTGGCGTTGA
*
1313 ATTATATGATTTTTCTGAGTATT
647 ATTATATGATTTATCTGAGTATT
* *
1336 GTCGCAAAAAATTGGGGAAAAAATTTTCGGGTAAGTTTTTTTCCAAATTTTAGCCGAAATCGTGC
1 GTCGCAAAAAATTGGGGAAAAACTTTTCGGGTAAG-TTTTTTCCAAATTTTAGCCGAAATCGTGT
*
1401 ACTAACCATCACGGTTTTTGGCTAAAAAT-CGTTTCGGGCCCTGACTCACTTTTGCATGATTTTT
65 ACTAACCATCACGGTTTTTGGCTAAAAATGCGTTTCGGGCCCTGACTCAGTTTTGCATGATTTTT
*
1465 GGCAGAAAGACTTCTCGAAATATCTATATTCATCTAATCAAATCTCTCAGCCACAATGGATTTAC
130 GGCAGTAAGACTTCTCGAAATATCTATATTCATCTAATCAAATCTCTCAGCCACAATGGATTTAC
* * *
1530 GGATTTATTTTTACGAGTATCTTAATCTTATTTCGATTTAATTAGAAATAAATTACAAGAAAAAA
195 GGATTTATTTTTACGAGTATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTTC-AGAAAAAA
1595 A
259 A
Statistics
Matches: 853, Mismatches: 65, Indels: 19
0.91 0.07 0.02
Matches are distributed among these distances:
665 1 0.00
666 121 0.14
667 225 0.26
668 165 0.19
669 258 0.30
670 83 0.10
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (669 bp):
GTCGCAAAAAATTGGGGAAAAACTTTTCGGGTAAGTTTTTTCCAAATTTTAGCCGAAATCGTGTA
CTAACCATCACGGTTTTTGGCTAAAAATGCGTTTCGGGCCCTGACTCAGTTTTGCATGATTTTTG
GCAGTAAGACTTCTCGAAATATCTATATTCATCTAATCAAATCTCTCAGCCACAATGGATTTACG
GATTTATTTTTACGAGTATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTTCAGAAAAAAAA
GGAAAAACGAAATTAGAAGCGTGAAAAACCCTAAAATATTTTTGGCGTTGAATTATATGATTTTT
CTAAGTATTGTGGCCAAAAAATTGTAGAAAAACTTTTCGCATCAAGATTTTCCAAAATTTTAACC
GAAATAGTGTACTAACCATCACGGTTTTTGGCTAAAAATACCTTTCGGGGCCCTGACTCAGTTTT
GCAATATTTTTGGCAGAAAGACTTCTCGAAATATCTATATTCATCTAATCAAATCTCTCAGCCAC
AATGGATTTACGGATTTATTTTTACGAGTATCTGAATCTTGTTTCAATTTAATTAGAAATAAATT
CAGAAAAAAATGGAAAAACGAAATTAGAAGCGTGAAAACCCTAAAATATTTTTGGCGTTGAATTA
TATGATTTATCTGAGTATT
Done.